9S8F | pdb_00009s8f

Amuc1755_S1_16 in complex with D-Galactose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		298	1.6 M Sodium Malonate Amuc1755 2,75 mg/ml with 100 mM D-Galactose

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 143.08	α = 90
b = 143.08	β = 90
c = 50.41	γ = 120

Symmetry
Space Group	P 64

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 S 16M		2021-09-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	1.0	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.1	71.54	100	0.999	15.8	9.9		344730

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16			0.666

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.1	71.54	34729	1753	99.994	0.168	0.1662	0.1762	0.2072	0.2118	37.145

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.55	-0.275		-0.55		1.785

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	15.664
r_dihedral_angle_6_deg	15.6
r_dihedral_angle_2_deg	9.772
r_lrange_other	7.314
r_lrange_it	7.31
r_dihedral_angle_1_deg	7.15
r_scangle_it	6.264
r_scangle_other	6.263
r_scbond_it	4.059
r_scbond_other	4.059
r_mcangle_it	3.901
r_mcangle_other	3.901
r_mcbond_it	2.757
r_mcbond_other	2.757
r_angle_refined_deg	1.732
r_angle_other_deg	0.589
r_nbd_refined	0.213
r_nbd_other	0.21
r_symmetry_nbd_other	0.196
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.154
r_metal_ion_refined	0.136
r_symmetry_xyhbond_nbd_refined	0.114
r_symmetry_nbtor_other	0.087
r_chiral_restr	0.082
r_symmetry_nbd_refined	0.071
r_bond_refined_d	0.007
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4214
Nucleic Acid Atoms
Solvent Atoms	116
Heterogen Atoms	13

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing